This is not really a bug for me, and it has always been like that. It is most visible since you have the merge of buffers, ie since version 0.3.0 (and to answer your question, yes it's still like that in 0.4.1 and development version).

The "day changed to" message is displayed on all buffers, so when buffers are merged you see it many times, it is normal behaviour.
If you unmerge server buffers (which is possible manually or via option irc.look.server_buffer), you'll see the message on each buffer.

As a workaround, you can hide such messages on irc servers (and keep it on WeeChat core buffer), with the command:

/filter add daychanged irc.server.* * ^Day changed to

The correct behaviour would be to not store this message as a line in buffer (which is current behaviour), but display dynamically this message between two lines when the date of two lines is different (so no need of a timer that displays these lines each day at midnight).
If you want such behaviour, feel free to add a task (feature request).